When babies are born, their immune systems are immature and require time for development and for immune function to improve. As they come in contact with environmental stimuli such as microbes, food particles, and other antigens, their immune systems learn how to differentiate “friend” from “foe”. They also learn how to effectively eliminate harmful substances (pathogens, toxins, etc.) from the body.

Problems arise when a baby’s immune system is not allowed to develop naturally.

The Gastrointestinal Tract

The headquarters of the immune system is the gastrointestinal tract. Since approximately 90% of known pathogens enter the body through the gastrointestinal tract, it makes sense that the vast majority of the immune system would be located here.

Within the first few months of an infant’s life, the gastrointestinal tract goes from being completely sterile (in the womb) to becoming colonized by hundreds, perhaps even thousands, of different types of microorganisms. These colonies of microorganisms are critical to immune system development and to fundamental biological processes such as digestion, nutrient assimilation, as well as detoxification.

The microorganisms in the gastrointestinal tract play a critical role in immune function. Good germs in the gut are known to provide essential “building blocks” for the human immune system, especially with regard to regulatory functions (the parts that keep the immune system “in check”). A lack of these essential building blocks can result in an immune system that cannot shut itself off, and can treat benign substances as “invaders”.

Relatively recently, scientists have discovered that disruptions to the development of the critical colonies of microbiota (microorganisms) in the gut can lead to a variety of immune system dysfunctions.

The Function of Germs in Immune Function

“Germ-free” animal models where animals are raised with sterile guts, have demonstrated that absence of good bacteria in their guts results in defective gut-associated lymphoid tissue (GALT), the tissue of the intestines that is considered the headquarters of immune function in our bodies. In other words, animals raised without gut bacteria develop immune systems that do not work properly, and thus the animals become very sick.

If you compare the number of human cells versus bacterial cells that each of us contains, we are more bacterial than we are human. Of all the cells in our body, we are about 10% human and 90% bacterial. If you compare the number of human genes in our body compared to bacterial genes, we are 1% human and 99% bacterial. All of these bacteria that we carry around weigh an average of 2 to 5 lbs. Other microorganisms that can inhabit the gut include yeasts, parasites, viruses, and protozoans.

The primary roles of “healthy” intestinal microorganisms include metabolism, defense, and immunomodulation (regulation of the immune system). The metabolic functions of good germs include (but are not limited to) vitamin synthesis, fermentation of carbohydrates, and energy production. Good germs are also necessary to protect the gastrointestinal tract from pathogenic invaders by producing bacteriocidins (highly specific “antibiotics”) and by competing with pathogenic organisms for food and space.

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